Naruto, Spartan-009
by anime-death-angel
Summary: After the sealing of the Kyubi, Naruto is transported to Reach in the Halo-verse where he is found by Dr. Halsey. Soon after Naruto is entered into the SPARTAN-II program. When he returns home, how will the Elemental Nations react to a SPARTAN. Naruto/OC(A.I.)


It was the night that Kyubi no Yoko attacked the village. People were dying left and right and the village was being torn apart from the Kyubi's rage. Its nine tails that could level mountains and cause tsunami's flared angrily as it tore through the village. But no one knew why the fox was attacking in the first place. It was safe to say that that the whole village was going to hell. But there were two people in the middle of it all.

"Minato-koi! You can't do this to him!" A woman with red hair said to the man named Minato who was her husband.

"Kushina-koi! We don't have a choice; with the way you are right now...the Kyubi will kill you!" Minato said to his wife as he held a bundle in his arms.

"Please! You can't do this to him! He can't lose us!" Kushina said as Minato shook his head.

"Don't worry! The village will-" He was cut off as he was knocked out from behind, and someone caught the bundle.

"Neither of you are dying here today!" An old man said wearing a black jumpsuit with an armored helmet and a gauntlet that covered his right hand, forearm, and elbow.

"Hiruzen! What the hell are you doing?" Kushina said as she saw him go through hand signs for a certain jutsu.

"The only thing I can do to help out right now!" He said as he finished the sequence.

"Wait! Are you-" Kushina said as she recognized the jutsu.

"Yes...I'm sorry Kushina...but at least this way...I know that the village and you two will be safe...and especially your son." Hiruzen said as they suddenly saw the Kyubi start to struggle with the chains that ensnared it.

"But...what about your family?" Kushina cried out.

"They are old enough to take care of themselves... my wife is dead… killed by the masked man… the only thing I can do now is secure the future for not only your son… but for also the next generation" Hiruzen said.

Kushina was speechless so she nodded her head, while tears fell from her eyes.

"Shiki Fujin!" The Sandaime Hokage yelled as the shinikami appeared behind him and tore its hand through the old kage and towards the Biju.

The chakra monster stopped struggling as its soul and power were split in two. One half was heading towards Hiruzen and into his gut as a strange symbol suddenly appeared on his gut area as he groaned in pain. Then he looked over and he noticed that the other half was heading towards the bundle in his arms. Which was now revealed to show a small blond baby boy with whisker marks on his face. And then the power went inside of him while the same strange seal appeared on his gut.

"SEAL!" Hiruzen yelled out as the Bijus body then faded away into dust as he smiled one final time.

Then the old man fell over dead, he had a smile on his face as he was devoured by the god of death.

And then the woman Kushina started to crawl over to the bundle.

"N-Naruto-chan." She said as she started to inch closer and closer to the bundle. But then something odd happened.

The bundle started to levitate in the air. Much to her shock, and then red Chakra started to hurl around it.

"NO!" She screamed as she figured the Biju was escaping.

Then baby Naruto started to cry as he suddenly started to glow a whitish color before suddenly disappeared in a flash of light. The woman stared at where the baby was...No she stared at where her baby was. Because in the last five minutes, her baby had become something hated in this world...and he was taken away from her.

"NO! NO! NO!" She screamed out as Minato started to come to his senses.

"K-Kushina-koi...what happened?" He said as he saw her crying.

"IT TOOK HIM! IT TOOK MY BABY!" Kushina yelled out as some Ninja started to show up and they saw Minato holding his wife as they both started to cry tears of sorrow.

**Another dimension: Year 2511: Planet Reach**

Dr. Catherine Elizabeth Halsey was easily recognized as one, if not the smartest woman of the 26th century. At age 12 she had already turned in her first Doctoral Thesis paper and a second Doctoral Thesis at 15. At 18 she supervised the creation of the template for third-generation "smart" AIs.

Now a year later she was going over the plans for the SPARTAN-II Program. During the past few years, insurrectionist attacks have been growing more and more steadily in the Outer Colonies causing demand for more efficient soldiers on the battlefield to reduce casualties. The problem was the subjects, who needed to be taught to understand military value, and the understanding of war; something that cannot be taught to enlisted soldiers. So they had no choice but to use children who after being identified through DNA gathered from the UNSC's civilian vaccination program in six years would be abducted and replaced with Flash Clones.

Currently the Dr. was taking a stroll outside the Reach Facility when her ears detected the unmistakable sounds of a baby crying in the bushes. Looking in she saw a blond haired baby that didn't look more than a few hours old.

Halsey picked up the baby, whose cries turned to whimpers. When she did as it opened its eyes, revealing them ocean blue. She also noticed three distinct whisker marks on his cheeks. She also saw the baby had an anklet that read in Japanese _Naruto_

"Let's get you inside little Naruto." Halsey said as she went back to the facility,

**10 minutes later**

After conducting numerous tests 'scientific and medical' Halsey found Naruto to be the healthiest baby she'd ever seen. However she could not find anything about his origins, no D.O.B, no social security number, nothing. It's as if the baby appeared out of thin air which was impossible.

Looking at the now sleeping baby, Halsey considered putting him in an orphanage where he'll hopefully be adopted but the child was the healthiest baby she'd ever seen making him a prime candidate for the SPARTAN-II Program.

**Timeskip 14 years later Year 2525**

Fourteen years have passed since Naruto arrived on Reach. When he was six, the UNSC had already identified 150 children for the program but only abducted and replaced 75. Their names were replaced with a combination of their first name and number with their last named erased. Naruto was named Spartan-009 Naruto.

Their first years of training were harsh. The SPARTANs endured a great deal of hardship during their training: they were placed into situations and drills that pushed their abilities to their very limit and beyond. Their hard training was complemented with high-level education, which included mathematics, science, reading, writing, and military tactics. Principles such as discipline, honor, and respect were literally drilled into their heads.

Though they were meant to fight against insurgents, SPARTANS now fought against a deadlier foe, The Covenant.

On February 11, humanity formally made contact with The Covenant and the Human-Covenant War began. Harvest was the first to fall with over 23,000 dead.

On March 9, the SPARTANS proceeded to the hardest part of their training to become super soldiers: the SPARTAN-II augmentation procedures. The procedure had them undergo rigorous chemical, physical and biological augmentations with only 34 Spartans successfully passing the alterations. However 33 of their brothers and sisters that they grew up and trained together died from the procedure with 12 more being permanently crippled.

On September 12th the Spartans were ready for their first mission.

**Time skip 16 years later Year 2541 (Naruto's age: 30)**

Spartan-009 Naruto did not even blink as he fired another round of bullets into a group of Grunts. The little grey squat aliens squealed then peeled over dead as blue blood spilled everywhere. The Spartan warrior rolled for cover as more Covenant forces fired at him while he emptied the empty magazine of his MA5D rifle and replaced it with a full one. Blue and green plasma fire flew through the air, flowed by needler ammo.

The Human-Covenant War had been raging across the galaxy for 16 years. During those years billions of lives have been taken, and many worlds Glassed, leaving them a barren wasteland. The Spartans were immediately sent to the front lines with more Spartans being created. In 2531 the SPARTAN-III program had been initiated with the purpose of created expendable soldiers from fallen colonies that were Glassed.

As the war progressed, two Spartans rose above the ranks faster than anyone could have anticipated, Spartan John-117 and Naruto-009. Both soldiers had proven to be effective leaders on the battlefield and received various medals in honor of their bravery and fighting skill. Both were also rewarded titles with John earning Master Chief Petty Officer from the Navy and Naruto earning Master Gunnery Sergeant from the Marines.

Because of his advanced healing, (which no one found out was because of the Kyubi) additional experiments were done to Naruto in order to accommodate an experimental MJOLNIR power suit he was outfitted with.

Naruto's suit was a white with black trimmed MJOLNIR Powered Assault Armor type V more commonly known as Extra-Vehicular Activity Armor or more commonly called EVA Armor. (Kelly in Halo: Legends, Noble 4 in Halo Reach, and Maine in Red vs Blue) The EVA armor came outfitted with three enhancements, cloaking, dome energy shield, and holographic projection. While the enhancements helped Naruto greatly, he had trouble using them, so Dr. Halsey gave him an experimental A.I. Allison that she created to help him function with his armor.

"Sergeant, above!"

Without looking up Naruto sidestepped out of the way from a stab from an energy sword of a Sangheili Elite and grabbed it's head in a head lock giving it a vicious twist, breaking it as the Elite fell to the ground dead.

Glancing back, Naruto saw more Elites recharge their plasma rifles, and he heard their throaty calls to the Grunts. Bumping into each other, the Grunt lines mixed and mingled as the little creatures tried to figure out which way to go. Willing his fingers to move faster, Naruto dug through the armor of the nearest marine body. Giving a loud sigh, he wrapped his fingers around the familiar round shape of a frag grenade. Grunting as heavy, hot plasma pounded into his back, the Sergeant ducked, rolled, and flipped around. Pulling the pin, the Sergeant smiled under his helmet, and then threw the grenade into the mass of armor and alien flesh.

Seconds after the grenade fell into the huddle of Covenant, it burst into a million pieces, sending shards of metal, plasma weapons, and alien bits flying. One Elite stormed into the pack of wailing Grunts, knocking aside any little aliens that stumbled into his path. Carefully watching the fast moving Elite, the Sergeant backed up a few feet before sliding his MA5 into its magnetic holster on his back and pulling his pistol from its resting place on the outside of his right thigh.

Running to meet the charging Sangheili, the Sergeant applied pressure to the trigger on his pistol. The bullets slammed into the Covenant's shields, pinged off, and clattered to the metal floor of the UNSC Cruiser. Emitting a rough, heavy roar, the 8' 10" Elite Minor rushed towards him. Sucking in a large breath, the SPARTAN allowed the giant Sangheili to bear down on him until he was a matter of feet away.

"Check mate." With a warm gurgle and bark of fright, the Elite Minor crumpled to the ground with a heavy thud, landing in a pile smothered in his own purple blood.

Taking a breather, Master Gunnery Sergeant SPARTAN Naruto-009 looked at the deceased bodies of his fellow marines, his men who he swore to protect.

Everything had gone wrong so fast.

Naruto was spending the day with his men who were either relaxing from all the fighting or training for the next battle on the Kage when his C.O. picked up an SOS from a nearby Marathon-class heavy cruiser.

The cruiser was known as The Poseidon which was carrying an experimental thermobaric bomb designed to wipe our Covenant bases.

The SOS reported that The Poseidon's engines had failed and needed the nearest cruiser 'which happened to be Naruto's' to deliver the bomb to Dr. Halsey. Naruto found the whole thing suspicious but none the less went to help.

When they arrived and docked, Naruto and his team went inside The Poseidon only to be ambushed by Covenant forces that had taken over the ship and laid a trap. Shortly after the ambush 3 CCS-class Covenant battlecruisers emerged from slip space and attacked The Kage and The Poseidon.

Naruto ran to the bridge of the Poseidon and activated the defenses to hold off the Covenant cruisers while the rest of his men retreated back to the Kage.

"Sergeant!"

Naruto looked towards the entrance of the bridge to see one of his recent graduate soldiers Elli standing at the door.

"Elli, what are you doing here? I ordered all Marines to fall back to the Kage!"

"I'm sorry Sir but we were intercepted by a squad of Elites. We need your help to…"

The young woman never finished her sentence as an energy sword pierced through her chest.

"NO!"

Naruto became a blur as he unsheathed his knife, rushed at the Elite that stabbed Elli, and jammed it in its throat. Not finished yet Naruto twisted the knife inside and yanked it out before stabbing the Elite again in the chest.

Turning his attention back to his comrade, Naruto saw Elli's eyes wide open, but no life in them. With a gently pass of his hand, Naruto closed Elli's eyes and collected her dog tags.

(Insert Gary Jules- Mad world)

"Naruto, the ship can't take any more damage." Allison said as an explosion rocked the Poseidon to further prove her point while Naruto placed a hand against the wall to steady himself.

He knew it was only a matter of time before The Poseidon was destroyed and the Covenant would focus their attention on The Kage. He thought back to when he was first assigned to The Kage five years ago, the many men and women he trained, who he fought with, who died. Those he failed to protect. Steeling his resolve he knew there was only one to do to protect his comrades.

Seconds later his com-link came to life.

"_Sergeant, the rest of the troops of made it back to The Kage. We're just waiting for you."_

"_I'm sorry sir…but I'm not coming back."_

"_What? Explain yourself."_

"_The Poseidon's nearly finished sir. It's only a matter of time before they focus their fire power on you. But you can make it out of here while I deal with the Covenant."_

"_How do you…" _Realization hit Naruto's C.O. like a bullet. _"The bomb?! You plan on detonating that thing? Forget it, I'm giving you an order to return at once."_

"_I'm sorry sir but I'm afraid I have to disobey that order."_

"_Master Gunnery Sergeant SPARTAN Naruto-009 you will return to The Kage as ordered and you will…"_

"_Please sir…We both know The Kage would survive the assault after they're finished with the Poseidon. Please…get our comrades out of here…get them safe…"_

"…_Very well Sergeant. We'll look for you after. After all SPARTANS never die…"_

"_They're just missing in action." _Naruto finished as he shut off his com-link and made his way to where the bomb was stored.

"Allison, download yourself to The Kage. They need your help more than me." Naruto said as he tore his way through a group of Grunts.

"NO, I won't leave you."

Naruto snapped the neck of an unlucky Grunt while stomping on the head of another, crushing it then turned back to his A.I. "I gave you an order, now go."

"I'm sorry sir but I'm afraid I have to disobey that order." Allison said with a smirk mimicking Naruto from earlier. "Besides I'm nearing the end of my life span and I want to spend my last few moments with you…"

Naruto stared at his A.I. and smiled under his helmet as he nodded and Allison went back into his head.

For the next several minutes, Naruto sprinted through the ship, killing any Grunts, Jackals, or Elites that stood in his way. Turning another corner, Naruto saw the room that contained the bomb. Just as he was about to enter, a large explosive caught him by surprise and threw him against the wall. Naruto grunted in pain as a piece of metal was lodged in his stomach. Pulling the metal piece out, Naruto threw it at a Jackal that appeared from the corner as it embedded itself in its head.

"Naruto!" Allison cried as the blond cough up a bit of blood while putting as much pressure as he could on his wound. The A.I. knew that her hosts advance healing could take care of almost any injure but not something this serious.

"I'm alright…just a flesh wound." Naruto said as he limbed towards the bomb. Upon reaching the device, Naruto began to arm it, never noticing an Elite sneaking up on him. Just as he finished, he felt a searing pain burn through his body as an energy sword pierced his shoulder. Turning he saw an Elite uncloak behind him with a smirk over its apparent victory. The smirk died when Naruto yanked out the sword, grabbed the Elite's throat, and shoved his M6G pistol in its mouth before firing, ending the aliens 'Great Journey'.

Hearing the countdown of the bomb behind, Naruto stood his ground and fired into another swarm of Covenant forces, not bothering to dodge the plasma or needler rounds hired at him as he knew this was his last stand.

"Allison…" Naruto called as he continued to fire at the enemy forces while the A.I. appeared next to him.

"Yes Naruto?"

"I want you to know that…after everything that's happened…you were my precious person."

"And you were mine…" Allison said looking like she could cry.

With those words said, the thermobaric bomb detonated, destroying what was left of the Poseidon and the all of the Covenant forces while the crew of The Kage watched from afar, saluting their fellow marines.

(End Gary Jules- Mad world)

**Limbo**

" argent… Sargent…up…Naruto, wake up…"

Naruto's eyes snapped opened as he woke up, floating in what appeared to be a white void that stretched for miles. He noticed that he still had his armor but only had his knife and his helmet was gone. Reaching up he felt his hair was not cut in military fashion anymore but was wild and spikey. What happened?

Looking around, he saw Allison looking at him with a relieved smiled.

"Glad to see your up, Sargent."

"Allison…" Naruto said, surprised to see his A.I. "Where are we?"

"I'm not sure. All I remember is the explosion before coming online here and waking you up."

"**I brought you here." **

Both turned to see a woman of unparalleled beauty standing before them barefoot. The woman was at least 5'6 with waist-length black silky hair, and beautiful forest green eyes. She had an impressive bust of C-cup, she also wore a royal looking white kimono with black trimming with a black sash around her waist.

Naruto immediately pulled out his knife.

"**Stand down, Naruto Uzumaki Namikaze. I mean no harm to you or your companion."**

That caught Naruto off guard. As far as he knew, there was no record of him having any family before the war. So why did this woman call him the last two names. The woman smiled as if reading his thoughts.

"**I know your true name because it is the one your parents, Kushina Uzumaki and Minato Namikaze gave you."**

"You are you?"

The woman smiled. **"I go by many names but you can call me Kami."**

"You honestly expect us to believe you're a Japanese goddess." Allison said. To prove her point, Kami waved her hand and suddenly they were standing in a beautiful forest.

"**Yes I do." **The deity said, smirking since they now believed her.

"Why did you bring us here?"

"**To offer you a choice, to go home in the Elemental Nations."**

Seeing the confused looks on the two, Kami waved her hand and an image of the Elemental Nations appeared before them. For the next several hours the image shifted, showing them Naruto's home that looked like 11th-18th century feudal Japan. The lands were split into various territories ruled by feudal lords or Daimyo's, each land had its own ninja village with Konoha, Kumo, Kiri, Suna, and Iwa being the strongest which was ruled by its own Kage. They saw ninja fight against each with swords, some casting illusions, and others using the elements themselves. The final images were of a giant nine-tailed fox that was attacking Konoha before it was sealed into a blond newborn, (they figured was Naruto) before it was transported to Reach where Dr. Halsey found him.

Both were quiet for a long time before Allison spoke. "Tell us, this fox creature, this…Kyubi no Yoko, is it the reason for Naruto's advanced healing factor?"

Kami nodded. **"Yes. You see Naruto the Kyubi was sealed into your mother Kushina before you. After you were born a mask man abducted your mother and released the Biju on Konoha which ultimately had it sealed in you. But despite its destructive power, the Kyubi is a gentle soul. The mask man was controlling it the entire time.** **Now I ask again, do you wish to go home Naruto."**

Naruto and Allison looked at eachother before nodding.

"**Good. Now hold still."** Before they could react, Kami waved her hand and two orbs a light appeared before flying right into the human and A.I.

Naruto immediately had the knife ready. "What did you do to us?"

"**Calm down Naruto. I simply gave you both knowledge of basic chakra control and techniques. Now one last thing." **Kami snapped her fingers a duffle bag with two large scrolls appeared in Naruto's hand. **"I believe these will come in handle for the future. Farewell and good luck Naruto Uzumaki Namikaze." **

With a final wave of her hand, Naruto and Allison were engulfed in a bright light before they disappeared to their new home. The Elemental Nations.

* * *

**I'm back. Hey everyone here's a new story for you. I've read a few Naruto/Halo crossovers and wanted to try one myself and here it is. To be honest I started this one back in October, I know a long time. **

**Anyway the next chapter will have Naruto in Wave where he will be 16 and (yes) Allison will be human. As for the scrolls, yes they're filled with both UNSC and Covenant weapons but Naruto will only use a select few. Let me know what you think :)**


End file.
